Miconazole is an imidazole antifungal agent, commonly applied topically to the skin or mucous membranes. The aim of this study was to examine the alternative method for gaining mechanism or the bimolecular changes caused by the possible teratogenic effects of Miconazole on mice fetus brain tissue using FTIR-Microspectroscopy. The mice were injected with Miconazole (60 mg/Kg) on gestation day 9. Fetuses were dissected on day 15 of gestation and morphological and histological studies on the fetus were carried out. Sections (10 μm) of control and Miconazole treated fetus brain tissue were used for FTIR measurement in the mid- infrared region. The results were shown by spectra 2nd derivative and also subtracting from control spectra. A lower intensity in the lipid (2800–3000 cm-1) and amid I (1600–1800 cm-1) regions of Miconazole treated mice fetus brain tissue was observed compared to the control mice fetus brain tissue. No major spectral shifting was observed at amide I band, amide II band and nucleic acid regions. As a conclusion, FTIR-Microspectroscopy can be a useful tool for teratogenic measurement with a unique ability to identify the modified bimolecular structures in mice fetus tissues.